4N9Y

Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E748Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FC2pdb entry 4FC2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62770.2M (NH4)2SO4, 16% PEG3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.6252.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.239α = 90
b = 91.103β = 90
c = 102.764γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35097.510.114271572648122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3790.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 4FC22.347.9226480141197.510.19920.19710.2398RANDOM31.2911
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.62-2.72.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.759
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg5.857
r_angle_refined_deg1.136
r_mcangle_it1.059
r_angle_other_deg0.733
r_mcbond_it0.607
r_mcbond_other0.607
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.759
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg5.857
r_angle_refined_deg1.136
r_mcangle_it1.059
r_angle_other_deg0.733
r_mcbond_it0.607
r_mcbond_other0.607
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4117
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing